QB Issue Resolution:

It may only stick when you create a new invoice and use it there… I don’t recall but I think its like that.

Resolution for Issue 'How can I make my custom template (for customer estimates) the default template?' available: Yes (Solved).
Source: Intuit Community forum.

How can I make my custom template (for customer estimates) the default template?: this issue or error code is a known issue in Quickbooks Online (QBO) and/or Quickbooks. Support for this issue is available either by self-service or paid support options. Experts are available to resolve your Quickbooks issue to ensure minimal downtime and continue running your business. First try to resolve the issue yourself by looking for a resolution described below. If it is a complex issue or you are unable to solve the issue, you may contact us by clicking here or by using other support options.

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